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This study aims to explore how gender and hukou-based residency status (urban vs. rural) jointly shape Klemera–Doubal Method (KDM)-based biological aging acceleration and to further investigate the cross-level interactions between community environment factors and gender. Although extensive research documents significant urban-rural and gender disparities in health—and acknowledges the influence of community environments—there is limited research on biological aging differences in China. Biological aging, which accounts for the interdependencies among multiple health indicators and relies on objective blood-based measures, helps reduce biases from different health expectations or under-treatment across groups. Nonetheless, research on how community factors affect biological aging acceleration, especially regarding potential gendered patterns, remains sparse. To address these gaps, we use data from the China Health and Retirement Longitudinal Study (CHARLS) to construct a KDM-based measure of biological age and a community infrastructure deficiency index to capture local environmental characteristics. We then employ multilevel models to examine the associations among KDM biological aging acceleration, gender, hukou-based residency, and community factors, incorporating cross-level interactions to determine whether there is a gendered influence pattern. Sensitivity analyses introducing an additional household-level clustering verify the robustness of our findings. Results show that females residing in urban areas, regardless of hukou type, exhibit significantly higher biological aging acceleration, while community-level infrastructure deficits and higher educational attainment each correlate with biological aging acceleration only among women. These patterns remain consistent even after accounting for household-level clustering, underscoring the critical role of community context and revealing a gender-specific influence on biological aging trajectories.